You can edit your homeworld planet with spaceship tools using a mod: AToAP Infinity [can be found in Sporedum archives]. Simply fly over the planet with another empire and edit the surface. Remember to save a game on a planet before you do this, because it will only delete the option to create new game on this planet. On existing save files works nicely!
The mod itself deletes the limit of tools, but also allows to edit any planet [including homeworlds, you can even blow them up, but it will corrupt save file]
I've seen weird things.